ChIP Foaming and other woes (archived)

ChIP - Foaming in sonication and other woes - (Jan/27/2005 )Hi all! I was wondering if anyone out there has got any trick to avoid foaming during sonication in the SDS lysis buffer for ChIP assays. Supossedly, placing the tip of the sonicator probe 13 mm below the surface of the liquid should avoid it, but is just not working on my hands. After 10 sec on the first sonication pulse a get lots of foaming, but I like to do longer pulses (20 sec) and foaming is supposed to denature the sample. For how long do you sonicate, and how many pulses? I'm using a Branson 250 sonicator.

Also, which type of vessel do you use for sonication? I use 2 ml eppendorf tubes, but the instruction manual of my sonicator recomends metal or glass vessels, better than plastic ones, because of heating considerations.

And last but not least, have you noticed differences in the sonication quality when using different cell lines? For some reason, I get really small fragments with 3T3 cells but not with 10T/2, and both of them are fibroblast cell lines. I don't change the conditions and sometimes I perform the experiments in parallel

Any thoughts or suggestions will be very welcome. Thanx!

-badcell- It is tricky to avoid foaming during sonication. I have tried both 1.5 ml (conival bottom) and 2 ml (round bottom) tubes and found 1.5 ml tubes are less likely to produce foam. In addition, according to this protocol, conical bottom improves sonication efficiency.

To avoid foaming, dip the probe all the way to the bottom of the tube. To avoid heating, hold the tube in ice water during sonication.

Hope that is useful.

-pcrman-Thanx alot for your answer, pcrman. I'm surprised to see that in the protocol you attach the sonication step is performed in RIPA buffer instead of the more astringent 1%SDS buffer. I've tried before to sonicate the sample in RIPA and the results were dismal, 10 kb DNA fragments. Maybe is because I used larger volumes (2-3 ml) corresponding to the final volume of the IP sample? I see that in this protocol the use smaller volumes and then dilute after sonication. I'll try that. Thanx again!

-badcell-

If you want to avoid foaming during sonication, cup horns are the way to go. They utilize indirect probe sonication, and are able to sonicate sealed vessels. Another advantage is that you can do multiple samples at once. The following link gives a better description:

Contact Misonix and they will be able to provide lab procedures for DNA shearing using the cup horn.

-sonix82-<!--QuoteBegin-badcell+Jan 27 2005, 12:12 PM-->

QUOTE (badcell @ Jan 27 2005, 12:12 PM)<!--QuoteEBegin-->After 10 sec on the first sonication pulse a get lots of foaming, but I like to do longer pulses (20 sec) and foaming is supposed to denature the sample. For how long do you sonicate, and how many pulses? I'm using a Branson 250 sonicator.<!--QuoteEnd--><!--QuoteEEnd-->Hi Badcell,

We use a Branson Sonifier B-30. I had real problems with foaming initially and I came to realise that the chromatin is not shearing properly when it foams up. We were using maximum settings on the sonifier with no luck.

So I tried lowering the settings with the same pulse times. The settings I used and were sucessful are a duty cycle of 30% and power setting to 3. I performed 15 continuous pulses for ten seconds each in 1.5 eppy tubes set in an ice bath to reduce the heat from sonication. We resuspend and sonicate our chromatin in RIPA buffer also.

I would suggest lowering the settings of the sonicator, that certainly stopped the foaming issue and still sheared the chromatin quite nicely.

The cells we work with are CHO hybrids but I am sure different cell lines behave differently. You could try optimising formaldehyde fixation times as I would think cell lines would behave differently to the fixation. (for our cells, 1% formaldehyde in media for 10 minutes exactly is suffice)

hope this helps!

Nick

-methylnick-

Thanks all of you for your suggestions, they really help!

Nick, I recently tried something similar to what you said: I fixed the cells using a lower concentration of formaldehyde than usual (0.5% for 10 min) and the shearing seemed to improve. I'll try your suggestion to decrease the power of the sonicator and increase the number of pulses.

Sonix, I thought water bath sonicators are not fit for shearing the DNA for ChIP assays, 'coz they're not powerful enough. I checked the webpage you indicated and it says that this cup horns are high intensity sonicators, but will the sample not heat up a lot during sonication? Heating of the sample during sonication, I heard, is supposed to denature the proteins, even break the formaldehyde bonds.

Thanx again both of you for your help!

-badcell-<!--quoteo-->

QUOTE <!--quotec-->Nick: I would suggest lowering the settings of the sonicator, that certainly stopped the foaming issue and still sheared the chromatin quite nicely.<!--QuoteEnd--><!--QuoteEEnd-->

Woe, this tip works and solved my foaming problem too! Previously I used a power setting of 15% (setting 3) and got foaming easily. After I lowered the setting to 10% (setting 2), I hardly got any foaming. Thank you Nick!

Here is my result with high and low power (volume 400 ul)

-pcrman-

no problemo pcrman,

I always thought that you needed the high setting to ensure proper chromatin shearing. but you don't

N

-methylnick-I'm using sonication to lyse E. COLI in a protein purification procedure. I'm trying to explain some strange results I observed.

I used a 25ml sample in a sonication test on duty-60%, intensity=6 for 5 minutes, taking samples every minute. Running the crude extract and the insoluble suspension on an SDS-PAGE gel for each time point showed very little difference in sonicating one minute and sonicating five minutes.

In addition, the insoluble and soluble bands were identical, which makes the presence of inclusion bodies less likely.

My lab is relatively new to sonication, so the hope is that the error is ours and not in the experiment. If sonication produced foaming, therefore denaturing the proteins, would this explain the results - at least in part?

-mwwall-

Hi mwwall,

Here we are talking about sonicating DNA. It seems that you are sonicating protein, right?

Once foaming occurs, sonicating efficiency goes almost to zero. I found your power setting is very high, have you experienced foaming? If yes, decrease your setting. Your are using 25 ml sample for sonication, that sounds to much to me. For ChIP sonication, the max volume I tried is 400 ul. Certainly the bigger the volume, the lower the efficiency.

-pcrman-

I just noticed the photo of you gel pcrman,

there have been some changes to the website, and the inclusion of photos with the messages is just awesome!!!

great to see lowering the settings worked for ya! seems so simple a change doesn't it?

Nick

-methylnick- I have been using the Upstate ChIP kit quite a while. Here are some tips which I think are important but not documentated in the protocol.

1) When taking the agarose beads using a yellow tip, cut off its end otherwise you will end up with dry beads only left (because the diameter of the beads is roughly the same of lumen of tip end.

2) After reverse crosslinking at 65C for 4 hr and one hour of proteinase K digestion at 45C, before going to phenol/chloroform extraction, you have to transfer the samples into a new tube because the cap no longer fit tightly on the tube after intensive heating. If you don't, your sample will leak when you vortex.

-pcrman-Thanx for all, although I haven't take ChIP in practice....There are many nice man tell me the tricky point in experiment...These help me to improve my exp.Thanks very much, Everybody...

There are several reasons for foaming, but there are some main:wrong vessel (wrong turbulence while sonication), too high power setting of the ultrasonic device, bad vibration behaviour of the system especially used microtips, wrong proceedure and system handling due to bad support by sales. But foaming is not the only problem to have best results!If you have any specific questions, do not hesitate to ask. I am very experienced in this by serving ultrasonic users in bio sciences since more than 45 years and Germany, but also worldwide.We usually propose to use a special set up based on a BRANSON SONIFIER 450 (and OEM units, not other manufacturers, because their over all performance and quality is poorer!) using a special cup horn including a cooling device for full temperature control.It is no problem to achieve highest ultrasonic power (is not combined with WATT of the power supply....!!!!) if necessary with full temperature control at around 2 - 4 °C. We are able to handle 7 test tubes at a time! Sample volumes smaller 100 µl is no problem!We know all systems on the market, so we can give recommendations for use of other units to recieve the best goals! Ask for more detailsAndreas

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The use of the right vessel is always a question of sample volume:
The conical tubes (1.5 ml) are good for sample volumes starting around 250 µl,
when using the round bottom one (2 ml) the minimum volume for successful sonication (without foaming - foam is killing hte performance down to approx 30 % left power only!) is around 1 - 1.3 ml.
The recommendation regaring glass or metal vessel is for heat transfer reason only - and usually given by people, who never worked with a system or may not even has seen one except in a brochure!
Count on people who are really experienced, but also know the technology background of the ultrasonic technology!
Ask me for more details in ultrasonic treatment!
Andreas

The use of the right vessel is always a question of sample volume:The conical tubes (1.5 ml) are good for sample volumes starting around 250 µl, when using the round bottom one (2 ml) the minimum volume for successful sonication (without foaming - foam is killing hte performance down to approx 30 % left power only!) is around 1 - 1.3 ml.The recommendation regaring glass or metal vessel is for heat transfer reason only - and usually given by people, who never worked with a system or may not even has seen one except in a brochure!Count on people who are really experienced, but also know the technology background of the ultrasonic technology! Ask me for more details in ultrasonic treatment!Andreas

Hi Andreas I need help with a sonication that is not working.. but I'm using a Misonix 4000 sonicator with a microplate cup horn and I need to shear the chromatin of mammalian cells (Saos2 and MCF-7).No results till now.I have been using a bioruptor in the past with NO problem.. but this Misonix is killing me!Help!

I use the Branson 450, which is similar to your 250. I also had problems with foaming initially but reducing the power output and increasing the number of pulses solved the problem.
Don't hold the tip too close to the bottom of the tube because you don't evenly shear your chromatin if you do.

Different cell lines certainly can behave differently in sonication based on their size and number. If your cells are small then you get more of them in a dish. The more cells you have the longer you need to sonicate for to fragment more chromatin. Seeing differences in the sonication efficieny between cell lines is certainly not unusual as a result.

Be careful with water bath sonicators because not all of them are powerful enough to shear DNA, and for some the power distribution around the horn isn't equal. Thus, seek some serious advise before getting one - and I don't mean advise from the company who will tell you anything to get you to buy their machine even if it's not suitable. From what I've heard, bioruptor's are supposed to be the best for ChIP, why the switch for whoever it was using the Misonix? First rule of science (and the first 10 rules for ChIP) - if it's working, don't change it!